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Tonight, PBS begins a three-part documentary (WGBH, Channel 2, at 9) called “God in America.’’ It’s thoughtful storytelling, but only part of the history of God in this new world, told by only some of the believers.

The opening night begins with a friar trekking in the desert Southwest, one of the missionaries who came with the conquistadors to bring the Gospel to native people, even as soldiers of that invading force came to extract gold and silver for themselves and their king back home. In that, they were not very different from other European settlers.

But the story of the Spanish settlement of New Mexico is exceptional, for the conversion of the Pueblo Indians was less successful than the friars had hoped. The Pueblo nation had its own religion, and the result was conflict, persecution, and rebellion. Because they could not persuade the native people to accept the Catholic faith as the one, true religion, either by preaching or force of arms, Spanish settlers withdrew from this frontier, though they long endured elsewhere in the new world. Alas, this is the only mention of native populations in the whole six-hour documentary, and they fared far less well in the European settlement from then till now.

The narrative turns to the Puritans of New England, and their drive to build “a city on a hill’’ that would be a light to the Christian nations they left behind. Though they sought freedom to read the Bible and determine its meaning unhampered by bishops or king, these settlers developed their own religious authorities. But their Puritan convictions carried seeds of new dissent that bloomed in the new settlement. One woman, Anne Hutchinson (portrayed here by Laila Robins), developed confidence in her personal experience of God and found a following as she talked about the need for believers to each experience the divine. She was seen by the ministers, and most of all by Governor John Winthrop (Michael Emerson), as a threat to the order of the settlement and was finally banished.

That was the dynamic the storytellers see in the nation’s religious history, the ever-changing conflict between the forms of religion and the personal experience of God. It was a war fought not only in church but also in the wider society. The first Great Awakening, a revival movement both in town and on the frontier in the middle of the 18th century, shook up religious authority and gave individual colonists a conviction of personal liberty that influenced the American Revolution 20 years later. And after the Constitution was adopted, it was largely conflict between established churches and the revivalist movements of the frontier that shaped the Bill of Rights and the guarantee of religious freedom.

Revival also gave birth to social reform: temperance movements, orphanages, schools. But the demand for religious conformity in the new public schools alarmed the newer arrivals of the 1830s and 1840s. In New York City, the fight was led by “Dagger John’’ Hughes (Jeffrey DeMunn), the rough-hewn archbishop who not only wanted religious freedom for his Catholic flock, but argued for it using the language of American democracy, demanding the rights the new arrivals were due under the promises of the new nation, promises shaped by the evangelical majority of the time.

Overall in these six hours, we see too little of Catholics, the nation’s largest Christian denomination. They reappear later, in the story of John F. Kennedy, whose campaign for the presidency raised alarm among conservative Protestants who saw a threat to their predominant role in American public life. Jews, too, get short shrift, with an episode on the second night on Isaac Mayer Wise, founder of Reform Judaism, who is presented as another evangelical reformer. And there is only fleeting mention of Mormons and Christian Science, none at all of Unitarians and New Age religion, whether the Transcendentalists of the 19th century or the new groups of the 20th. Buddhists and Hindus and Muslims are mentioned only as immigrants, not as faiths that promoted their message and found a general audience.

Stay for the storytelling, most of all for the second installment, which tells of Abraham Lincoln (Chris Sarandon), who like many presidents, was not a conventionally religious man and was skeptical of his parents’ church. But he lived through the most terrible conflict in the nation’s history, more than 600,000 dead, with both sides deeply convinced that God was on their side. Lincoln came to see the war as a divine trial for a nation guilty of the sin of slavery, a conviction that moved him to issue the Emancipation Proclamation, acting against all good advice by his Cabinet.

Stay, too, for the third night, when the nation’s still incomplete civil rights battle is played out, led by evangelical Christian leaders and fought by evangelical Christian leaders. And there is a good retelling of the rise of Billy Graham, who made himself chaplain to presidents and tried to secretly scuttle JFK’s chances at the White House.

This sprawling six hours tells an American story, our story, no matter where we come from or where we are heading. You need to know it.